Mechanical response of the RecA nucleoprotein filament to increasing D-loop length

This repository contains the files and data associated with the article: Mechanical response of the RecA nucleoprotein filament to increasing D-loop length by Afra Sabei, Chantal Prévost, Mara Prentiss, Claudia Danilowicz, Sébastien Neukirch, and Alexandre Détruit. DESCRIPTION Trajectories: Contains the structural files for the RecA nucleoprotein filaments (NPFs) with varying D-loop sizes (9bp, 12bp, 15bp, 21bp, 36bp, 45bp, and 54bp). Initial structures were derived from the CryoEM structure (PDB: 7jy9). Filament expansion was performed by replicating subunits using the Heligeom module of the PTools library. Models are named based on the number of stable heteroduplex base pairs(replicas are uploaded separately). Parameters: All-atom Molecular Dynamics (MD) simulations were prepared using the VMD auto PSF builder (VMD 1.9.2). Systems were solvated in a TIP3P water model with a physiological ionic concentration of 0.15 mol/l. Simulations were performed using NAMD (versions 2.12 and 2.13) and the CHARMM36m force field including CMAP corrections. Conditions included periodic boundary conditions via PME, 2 fs time steps (SHAKE algorithm), and temperature/pressure regulation via Nosé-Hoover-Langevin piston. Scripts: Contains the following Python scripts for modeling and analysis: construction_bioarxiv.py: Script for the construction of the NPF models. cmap_bioarxiv.py: Post-processing script for generating contact maps. site_II_bioarxiv.py: Post-processing script for site II distance calculations. REFERENCES [1] H. Yang, C. Zhou, A. Dhar, and N. P. Pavletich. Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures. Nature, 586(7831):801–806, 2020. [2] A. J. Conover, C. Danilowicz, R. Gunaratne, V. W. Coljee, N. Kleckner, and M. Prentiss. Changes in the tension in dsDNA alter the conformation of RecA bound to dsDNA-RecA filaments. Nucleic Acids Res, 39(20):8833–43, 2011. [3] J. C. Bell and S. C. Kowalczykowski. Mechanics and single-molecule interrogation of DNA recombination. Annu Rev Biochem, 85:193–226, 2016. [4] A. Saladin, S. Fiorucci, P. Poulain, C. Prévost, and M. Zacharias. PTools: An opensource molecular docking library. BMC Struct. Biol., 9:27–37, 2009. [5] B. Boyer et al. An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. PLoS One, 10(3):e0116414, 2015. [6] B. Boyer, B. Laurent, C. H. Robert, and C. Prévost. Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. Bio Protoc, 11(14):e4097, 2021. [7] A. D. Mackerell Jr, M. Feig, and C. L. Brooks 3rd. Extending the treatment of backbone energetics in protein force fields... J Comput Chem, 25:1400–1415, 2004. [8] J. C. Phillips et al. Scalable molecular dynamics with NAMD. J Comput Chem, 26:1781–1802, 2005.